A common reason for the Index Status count to go down at the "update" is that an alternate version of the website is verified in Webmaster Tools. A simple way to double-check that is to do a site:-query for just your domain name (eg https://www.google.com/#q=site:fish.com ), and to see which version is shown. If the www-version is shown, then that's the version where most of your data will be. If you want to be on the safe side, just verify both of them.
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